Fords do not set misfire codes until it gets REALLY bad, As in the PCM can no longer manipulate things to prevent Catalyst damage.
In the Ford/Vehicle specific data display....There will be a Misfire PID, Reads (Yes/No)
*Test drive the vehicle....Apply varying amounts of load to the engine.
*Watch the Misfire PID to switch from "No" to "Yes".
*Try to make it read "Yes" as much as possible....If it misfires at 20% load at 30 MPH, Try to recreate that a few times to establish a pattern.....If it misfires again at 40% load at 60 MPH, Recreate that a few times, Again......Patterns, Patterns, Patterns!!
*If you feel a misfire while it says "Yes".....And it's repeatable....You have a misfire!!
*There are some things that can prevent the misfire monitor from running! Like low fuel level, Open Loop, DTC set. etc etc.
If it just flashes "Yes" every once in a while in no repeatable fashion....This test has provided inconclusive results.
The next step is to use Mode $06 (On Board Monitored Systems), This is available on most decent scan tools.
*Select test $53
*The "Components" will be numbered $01 thru $08....These are Cylinder ID numbers. $01 is cylinder #1 & $08 is cylinder #8.
*Scroll through the components & find the "Failed" component, This will be the offending cylinder.
Fords are NOTORIOUS for Coil degradation that cause random/load specific misfires, They also just flat fail....Obviously not the case here.
If you find a bad coil....Replace it with Motorcraft!
Putting new Boots on these Coils is a stop-gap repair at best if one or more was leaking Secondary voltage. Seeing what that does to the Primary Control Amperage waveform makes you wonder how the Coils put up with secondary leakage as well as they do!!
Fords have the Coil Transistors built into the PCM & can be damaged if ran long enough with faulty coil/s! I don't understand the theory behind that engineering decision as GM & Toyota for example use COP coils with built in Transistors. Not only do they generally last the life of the vehicle.....The PCM is never in danger.